AT1 markers are expressed in right while AT2 cells in the left
Check the expression of AT1 and AT2 markers
May be AT1 markers are started to expresse in cluster 5 then 2 and then 7.
Looking at 'Ager' expression with diff map which is more focused on trajectory findings.
Cluster 0,3,4,6 has high AT2 markers. while is basically all left side of part on UMAP. While in the right side of the UMP, specially in middle starting with cluster 5,2,7 expresses in AT1 markers.
Cluster 0 most contains DAY 14 cells and some DAY 10.
in my opinon, the most there two While now we see two seperate trends in UMAP for clusters, ie. AT1 and AT2. Combinations of clusters interesting to look at are : cluster 0,7,8. Another trend is : 1,2,3 and a seperate trend : cluster 4,5,6
Looking for cluster 5, as it looks like the starting point for cells to divide into two paths and making two seperate trends in the cluster. Lets find out which cell types they are first.
Stem cell markers are expressed highest in cluster 7, then cluster 8 and lastly cluster 1. Lets look which DAY it falls in, expression of genes in this cluster.
Reload the object that computed differential expression by comparing to the rest of the groups.
STOP HERE AND DO NOT RUN BELOW. REFERE TO SUBCLUSTER 2 VELOCITY NOTEBOOK. FOR REPEATING ABOVE RESULTS YOU SHOULD LOAD SAVED H5AD FILE : "controls_after_filter_Clustering_velocity_original_resolution_0.4.h5ad"